无法使用颜色将系统发育树保存为pdf

Question

I am trying to save my phylogenetic tree with coloured branches using discrete data, everytime I do the pdf() function and then try to open it I get a pdf error. This is the code I am using

tree = read.nexus("phylo.1966")
tree3<-read.csv("BBS1966.2015.pgls.csv",row.names = 1)
tree3<-setNames(tree3[,1],rownames(Nesting))
cols<-setNames(palette()[1:6],levels(Nesting))
Nesttree<-make.simmap(drop.tip(tree2, setdiff(tree2$tip.label,names(Nesting))),Nesting, model = "SYM"
plotTree(Nesttree,cols,type="fan",fsize=0.8,lwd=3,ftype="i")
add.simmap.ledgend(colors=cols,x=0.9*par()$usr[1],y=0.9*par()$usr[4],prompt=FALSE,fsize=0.9)
pdf("Nesting1.pdf", width = 100, height = 100)
dev.off()

however, if I place the pdf function before the plotTree function it will open but no color is added to the tree. tree2 is from a code used previously which just took my original tree and added the subspecies to make a new tree.

Also if I try to manually save the plot as a jpeg the size of the tree remains the same but the plot area will change to the size I chose, so it looks small and super crowded.

Thank you for any help. This is the image I produce after using the corrected code

Answer 1

As I commented you can manually adjust the width and height of images if you images is crowded. You can use any device in place of jpeg (eg PDF) for pdf however you don't need to set height or width.

jpeg("filename.jpeg", height = 1080, width =1080)
plotTree(Nesttree,cols,type="fan",fsize=0.8,lwd=3,ftype="i")
add.simmap.legend(colors=cols,x=0.9*par()$usr[1],y=0.9*par()$usr[4],prompt=FALSE,fsize=0.9)
dev.off()